Summary
AlphaFold3’s internal representation becomes lower-dimensional as the Pairformer processes MSA-conditioned inputs. The Pairformer compresses diffuse coevolutionary information into a compact pair-space geometry from which structural and biophysical features are increasingly linearly decodable (1).
See also
- AF3-generation methods incorporate MSA information exclusively into the pair representation
- Triangular updates are dispensable for structure prediction
1.
Feldman J, Skolnick J. AlphaInterp: Mechanistic Interpretability of AlphaFold 3 Reveals How Evolutionary Information Shapes Protein Structure Prediction. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.04.22.720175